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blastdoor
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Linux+Threadripper plunge

Fri Sep 07, 2018 1:14 pm

After using Macs exclusively for over 10 years, I'm venturing back out into the non-Apple world. I just ordered a custom built Threadripper 2990wx running Ubuntu.

I've never used Linux before on my own hardware (I had used Windows before going Mac). My plan is to use this primarily for running many (64, to be specific) parallel instances of R. But I'm also thinking I'll use it as a Plex server.

One thing I'll need to do is remote into this new system (I plan to stash it in the basement and remote in from my iMac). Any suggestions for software for doing that?

Are there other folks around here who have given up waiting on Apple to update their Pro hardware and moved on to Linux? If so, can you share any tips/tricks for integrating a Linux box into an otherwise Apple household?
 
chuckula
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Re: Linux+Threadripper plunge

Fri Sep 07, 2018 1:29 pm

What a pirate. You're even running Arrrrrrrrgh.

I just ordered a custom built Threadripper 2990wx running Ubuntu.


A real Jedi builds his own lightsaber, but I'll overlook that.

One thing I'll need to do is remote into this new system (I plan to stash it in the basement and remote in from my iMac). Any suggestions for software for doing that?


Yeah, that's easy: SSH.
If you need graphics because you've accepted the Apple Koolaid about all that stuff, there are several options. This guy has a post about VNC from Mac to Linux that might be helpful: https://www.youtube.com/watch?v=r-lQ1VjY02s

When it comes to remote graphics protocols, I personally recommend getting RDP working, which can even interact with the X11 stack although it can be a little complicated.

As for a plex server, that's not my bailiwick but as long as it coexists with your other software it has its own remote interface that's media playback specific.
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blastdoor
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Re: Linux+Threadripper plunge

Fri Sep 07, 2018 1:44 pm

Yeah, I used to build my own, but I'm done with that, at least until there aren't any kids in the house. There just isn't enough time.

Thanks for the link -- I will check it out!

chuckula wrote:
What a pirate. You're even running Arrrrrrrrgh.

I just ordered a custom built Threadripper 2990wx running Ubuntu.


A real Jedi builds his own lightsaber, but I'll overlook that.

One thing I'll need to do is remote into this new system (I plan to stash it in the basement and remote in from my iMac). Any suggestions for software for doing that?


Yeah, that's easy: SSH.
If you need graphics because you've accepted the Apple Koolaid about all that stuff, there are several options. This guy has a post about VNC from Mac to Linux that might be helpful: https://www.youtube.com/watch?v=r-lQ1VjY02s

When it comes to remote graphics protocols, I personally recommend getting RDP working, which can even interact with the X11 stack although it can be a little complicated.

As for a plex server, that's not my bailiwick but as long as it coexists with your other software it has its own remote interface that's media playback specific.
 
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Re: Linux+Threadripper plunge

Fri Sep 07, 2018 2:37 pm

Plex is fairly straightforward to manage via the GUI if need be. I've only had to login to mine once or twice when an upgrade blew up on me.
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Re: Linux+Threadripper plunge

Fri Sep 07, 2018 2:41 pm

I remember the install process being fairly straightforward also. After the package is installed you bring it up in a browser and follow the steps to finish the configuration.
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dragontamer5788
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Re: Linux+Threadripper plunge

Fri Sep 07, 2018 2:49 pm

If you're used to "brew", then you'll be able to "aptitude install" no problem.

The key is figuring out which clients work well on Mac's side. I don't use a Mac, so I don't really know the best remote desktop. But there are a lot of options out there that will make a setup like yours work. Best of luck!!
 
blastdoor
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Re: Linux+Threadripper plunge

Fri Sep 07, 2018 2:54 pm

Thanks -- I have a Plex client for my AppleTV which has worked fine using my old Mac Pro as the server.

dragontamer5788 wrote:
If you're used to "brew", then you'll be able to "aptitude install" no problem.

The key is figuring out which clients work well on Mac's side. I don't use a Mac, so I don't really know the best remote desktop. But there are a lot of options out there that will make a setup like yours work. Best of luck!!
 
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Re: Linux+Threadripper plunge

Fri Sep 07, 2018 3:26 pm

I'd likely rather SSH/VNC/whatever, but the remote desktop app for macOS isn't completely awful either if you just want a super simple way to get in without much set up.

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ptsant
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Re: Linux+Threadripper plunge

Fri Sep 07, 2018 4:29 pm

blastdoor wrote:
After using Macs exclusively for over 10 years, I'm venturing back out into the non-Apple world. I just ordered a custom built Threadripper 2990wx running Ubuntu.

I've never used Linux before on my own hardware (I had used Windows before going Mac). My plan is to use this primarily for running many (64, to be specific) parallel instances of R. But I'm also thinking I'll use it as a Plex server.

One thing I'll need to do is remote into this new system (I plan to stash it in the basement and remote in from my iMac). Any suggestions for software for doing that?


I use a macbook pro to interface with an aging Kaveri 860K server with 32GB of RAM/8TB HDD, mostly for R and bioinformatics. I don't quite see why you need 64 instances of R (you know that you can run parallel code in R?) but I'm sure you have excellent reasons.

Anyway, the obvious way to connect is with ssh. You install ssh in the macbook, copy your public key from the mac to the server then login with ssh server_ip (google how to this, for example https://www.digitalocean.com/community/ ... sh-keys--2). This also allows you to run rsync transparently (without passwords), something that I use heavily to synchronize files to/from the mac. Finally, you can channel X over ssh--with some added configuration--meaning that you can display X apps running on the server on the mac (not in the console, but in their own windows with Xquartz). Unfortunately, X applications are usually a bit ugly in the OS X environment or maybe I never cared enough to tune their appearance. I don't use that feature heavily, but it works and you might be interested.

I'm running a lot of custom R packages so I would urge you to install a complete development environment (including C/C++, fortran and all the obscure stuff that R may require). I also generally don't rely on package updates for R from ubuntu, but rather prefer to install R from source, the reason being that I need to control exactly what version I run and how it is compiled. Having multiple docker containers can help with this, if you need to have multiple R environments for multiple projects. I don't use this very often, but it's probably worth it if you have complex needs (ie R version xx + packages for one project and R version yy + other packages for another project).

Finally, my recent experiences with linux mint have been more favorable than with ubuntu. I installed ubuntu 18.04 only then to do a clean install of linux mint a few weeks ago. Our other systems at the lab had been running ubuntu 16.04 and the upgrade to 18.04 was also quite painful. Your mileage may vary.
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blastdoor
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Re: Linux+Threadripper plunge

Sat Sep 08, 2018 5:53 am

Very helpful -- thanks!

Perhaps I misused the word "instances", but what I really mean is that I use the mcparallel command from the parallel package to spin off a bunch of processes to run Monte Carlo simulations.

ptsant wrote:
blastdoor wrote:
After using Macs exclusively for over 10 years, I'm venturing back out into the non-Apple world. I just ordered a custom built Threadripper 2990wx running Ubuntu.

I've never used Linux before on my own hardware (I had used Windows before going Mac). My plan is to use this primarily for running many (64, to be specific) parallel instances of R. But I'm also thinking I'll use it as a Plex server.

One thing I'll need to do is remote into this new system (I plan to stash it in the basement and remote in from my iMac). Any suggestions for software for doing that?


I use a macbook pro to interface with an aging Kaveri 860K server with 32GB of RAM/8TB HDD, mostly for R and bioinformatics. I don't quite see why you need 64 instances of R (you know that you can run parallel code in R?) but I'm sure you have excellent reasons.

Anyway, the obvious way to connect is with ssh. You install ssh in the macbook, copy your public key from the mac to the server then login with ssh server_ip (google how to this, for example https://www.digitalocean.com/community/ ... sh-keys--2). This also allows you to run rsync transparently (without passwords), something that I use heavily to synchronize files to/from the mac. Finally, you can channel X over ssh--with some added configuration--meaning that you can display X apps running on the server on the mac (not in the console, but in their own windows with Xquartz). Unfortunately, X applications are usually a bit ugly in the OS X environment or maybe I never cared enough to tune their appearance. I don't use that feature heavily, but it works and you might be interested.

I'm running a lot of custom R packages so I would urge you to install a complete development environment (including C/C++, fortran and all the obscure stuff that R may require). I also generally don't rely on package updates for R from ubuntu, but rather prefer to install R from source, the reason being that I need to control exactly what version I run and how it is compiled. Having multiple docker containers can help with this, if you need to have multiple R environments for multiple projects. I don't use this very often, but it's probably worth it if you have complex needs (ie R version xx + packages for one project and R version yy + other packages for another project).

Finally, my recent experiences with linux mint have been more favorable than with ubuntu. I installed ubuntu 18.04 only then to do a clean install of linux mint a few weeks ago. Our other systems at the lab had been running ubuntu 16.04 and the upgrade to 18.04 was also quite painful. Your mileage may vary.
 
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Re: Linux+Threadripper plunge

Sun Sep 09, 2018 10:55 am

ptsant wrote:
Finally, you can channel X over ssh--with some added configuration--meaning that you can display X apps running on the server on the mac (not in the console, but in their own windows with Xquartz). Unfortunately, X applications are usually a bit ugly in the OS X environment or maybe I never cared enough to tune their appearance. I don't use that feature heavily, but it works and you might be interested.

I'm not running a Mac, but "ssh -Y <hostname>" sets everything up and X things just appear back on your display automagically without any need for special configurations on Linux.
 
ptsant
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Re: Linux+Threadripper plunge

Sun Sep 09, 2018 12:01 pm

notfred wrote:
ptsant wrote:
Finally, you can channel X over ssh--with some added configuration--meaning that you can display X apps running on the server on the mac (not in the console, but in their own windows with Xquartz). Unfortunately, X applications are usually a bit ugly in the OS X environment or maybe I never cared enough to tune their appearance. I don't use that feature heavily, but it works and you might be interested.

I'm not running a Mac, but "ssh -Y <hostname>" sets everything up and X things just appear back on your display automagically without any need for special configurations on Linux.


On the mac you need to install the X windows system (Xquartz: https://www.xquartz.org/ ). The server must also allow X11 connections in the sshd config (/etc/sshd/sshd_config), which is not always default. But otherwise not exceptionally complicated.
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Re: Linux+Threadripper plunge

Tue Sep 11, 2018 6:52 pm

On Plex, it's simple enough to set up the server side on a Debian-based distro, and for the most part, it's not resource-hungry unless it needs to do lots of transcoding (think playback of non-x264 sources on iOS devices, or playback with vobsub subtitles enabled on same if you tend to go that route while ripping).

Ours runs in an Ubuntu server VM on our home KVM host, but the end result is largely the same regardless of whether it's run directly on hardware or virtualised.

Assuming there's no interest in running the beta version, I've found that the simplest way to install and maintain the media server is to set up their apt repository, which (after an 'apt update') reduces the install to a simple 'apt install plexmediaserver'. Subsequent updates are then installed the same way.

Apologies for the lack of a direct link, but I don't tend to use the forums, and haven't yet earned the right to post links. Plex's documentation on their repositories is here:

support.plex.tv/articles/235974187-enable-repository-updating-for-supported-linux-server-distributions/
 
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Re: Linux+Threadripper plunge

Tue Sep 11, 2018 8:35 pm

A few tips ...

1. Don’t use SAMBA for network sharing ... use NFS. Samba performance sucks and security wise it sucks too.
2. Don’t use the MacOS filemanager to do large file transfers (either file “quantity” or “size”). Use “rsync”, as someone mentioned earlier. “rsync” preserves file date creation (unlike “scp”) which I find very useful.
3. You may know this but ... I insert “time” in front of many of my console commands, so u can keep track of how long certain tasks take.
4. I also use “watch -n 3” inserted before many commands to “watch” when changes r made; it’s very useful for troubleshooting
5. I use TMUX too ... that way I can have a hundred terminal sessions open and easily manage and switch between them! This is frigging ... awesome!
6. VIM too ... that way I can code on my remote server with a CUSTOM BUILT IDE. Most (ALL?) development IDEs charge for this ability.

It took me many years to learn these lessons ... I could go on for hours ... Good luck!

Ubuntu 18.04 LTS is really great. I switched to Linux Desktop in 2005 and never looked back. Though, all our phones, laptops and tablets are APPLE!

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Re: Linux+Threadripper plunge

Wed Sep 12, 2018 4:42 am

GuruBill wrote:
1. Don’t use SAMBA for network sharing ... use NFS. Samba performance sucks and security wise it sucks too.

If there's any need to support remote filesystem mounts for Windows clients, SAMBA is kinda necessary... unless you want to install 3rd party NFS clients on the Windows systems. If all you need is to move files back and forth (no need for an actual remotely mounted filesystem), WinSCP is a good option for Windows clients. (OP doesn't mention a need to support Windows clients at all, but it'll probably come up.)

For scenarios where performance isn't critical and simplicity (no setup) and security are paramount, sshfs (userspace filesystem driver which uses ssh as the underlying transport) is a useful option between Linux systems.

GuruBill wrote:
2. Don’t use the MacOS filemanager to do large file transfers (either file “quantity” or “size”). Use “rsync”,

Another vote for rsync. It's the "Swiss army knife" of file transfer/sync. Hardly a day goes by that I don't use it. Although people tend to think of it as a tool for doing remote file transfers, it is useful for moving files around on local disks as well, since it only copies what has changed (it's great for syncing contents of a local directory to slow media like a thumbdrive).

GuruBill wrote:
as someone mentioned earlier. “rsync” preserves file date creation (unlike “scp”) which I find very useful.

Scp will preserve the file dates if you use the "-p" option.
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Re: Linux+Threadripper plunge

Wed Sep 12, 2018 7:39 am

GuruBill wrote:
A few tips ...
1. Don’t use SAMBA for network sharing ... use NFS. Samba performance sucks and security wise it sucks too.


Umm, NFSv3 and lower can be incredibly insecure. Like, clear text insecure. It has more to do with how you configure it.

Also, SMB 3.1 and later are not as slow as the older versions. In home use you'd be hard pressed to find a real world difference.
 
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Re: Linux+Threadripper plunge

Wed Sep 12, 2018 10:45 am

DragonDaddyBear wrote:
GuruBill wrote:
A few tips ...
1. Don’t use SAMBA for network sharing ... use NFS. Samba performance sucks and security wise it sucks too.

Also, SMB 3.1 and later are not as slow as the older versions. In home use you'd be hard pressed to find a real world difference.


I was wondering about this. For my XigmaNAS install, I forced the latest SMB, and it doesn't seem to be a limiting factor- though it also doesn't seem to be as fast as Storage Spaces. I don't think the write caching on XigmaNAS with ZFS is working as well as it did with Storage Spaces, and I might look for another solution.

I was damn near set on OpenMediaVault too, until I found that their ZFS implementation (through the Proxmox kernal) doesn't support caching at all :/.

Tempted to go back to Storage Spaces, since I'm mostly Windows.

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ptsant
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Re: Linux+Threadripper plunge

Wed Sep 12, 2018 10:59 am

DragonDaddyBear wrote:
GuruBill wrote:
A few tips ...
1. Don’t use SAMBA for network sharing ... use NFS. Samba performance sucks and security wise it sucks too.


Umm, NFSv3 and lower can be incredibly insecure. Like, clear text insecure. It has more to do with how you configure it.

Also, SMB 3.1 and later are not as slow as the older versions. In home use you'd be hard pressed to find a real world difference.


On my system SMB saturates gigabit ethernet with relative ease during backups. Of course, I'm not running complicated scenarios with multiple users running multiple tasks etc, but I wouldn't change to NFS only for performance reasons.
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Re: Linux+Threadripper plunge

Wed Sep 12, 2018 11:25 am

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blastdoor
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Re: Linux+Threadripper plunge

Mon Sep 24, 2018 7:35 pm

After several 2 steps forward, 1 step back experiences, I now have my 32 core ThreadRipper Linux system up and running -- I'm looking at a System Monitor with 64 logical CPUs running close to flat out!

There's a ton I need/want to do, but one question in case anybody might know..... I'm using RealVNC and having some difficulty when I try to go headless on the Linux system. Everything works fine so long as a monitor is plugged in, but when I go headless things start to degrade and then the UI becomes unusable.

Might anybody have ideas for what to do about that?

i'm also using ssh, and I might end up making that my primary method of connecting, but ideally I'd like headless VNC to work.
 
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Re: Linux+Threadripper plunge

Mon Sep 24, 2018 8:26 pm

It’s been awhile, but I remember having to manually load X when running headless so VNC could connect. Maybe in init.d?
Last edited by Usacomp2k3 on Mon Sep 24, 2018 10:17 pm, edited 1 time in total.
 
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Re: Linux+Threadripper plunge

Mon Sep 24, 2018 8:54 pm

There's a way to start a VNC server that doesn't mirror a physical display; it just uses a virtual framebuffer in system RAM. Unfortunately it has been a few years since I've done that, so I don't have the procedure memorized any more; but I know it is possible. GIYF...
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Re: Linux+Threadripper plunge

Tue Oct 16, 2018 1:32 pm

blastdoor wrote:
After several 2 steps forward, 1 step back experiences, I now have my 32 core ThreadRipper Linux system up and running -- I'm looking at a System Monitor with 64 logical CPUs running close to flat out!

There's a ton I need/want to do, but one question in case anybody might know..... I'm using RealVNC and having some difficulty when I try to go headless on the Linux system. Everything works fine so long as a monitor is plugged in, but when I go headless things start to degrade and then the UI becomes unusable.

Might anybody have ideas for what to do about that?

i'm also using ssh, and I might end up making that my primary method of connecting, but ideally I'd like headless VNC to work.


The easiest solution I can think of, is to buy a dummy plug.

https://www.amazon.com/Headless-Display ... B06XT1Z9TF

The plug pretends its a 1920x1080p monitor. I don't know if this plug is good (I just picked the first one from Amazon), but they're made by a lot of manufacturers. Does anyone know a good brand-name to recommend for this problem?

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